Variant report

Variant	rs4547577
Chromosome Location	chr2:133393808-133393809
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10179167	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10179785	0.82[ASN][1000 genomes]
rs10189715	0.80[CEU][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs10208154	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1131671	0.86[JPT][hapmap];0.82[TSI][hapmap];0.84[ASN][1000 genomes]
rs13028563	0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs17396537	0.82[ASN][1000 genomes]
rs3738842	0.84[ASN][1000 genomes]
rs4340582	0.84[ASN][1000 genomes]
rs4547578	0.84[ASN][1000 genomes]
rs6430370	0.86[JPT][hapmap]
rs7558213	0.82[ASN][1000 genomes]
rs7558730	0.88[ASN][1000 genomes]
rs7567602	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7603894	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7603926	0.89[ASN][1000 genomes]
rs7608591	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011421	chr2:132895241-133682185	Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv875137	chr2:133167263-133714142	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv1014306	chr2:133252736-133402581	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv535925	chr2:133252736-133402581	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv583155	chr2:133253386-133415170	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv583158	chr2:133316092-133862100	Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4547577	NCKAP5	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:133379400-133395800	Weak transcription	Gastric	stomach
2	chr2:133389400-133403200	Weak transcription	Brain Anterior Caudate	brain
3	chr2:133390000-133401000	Weak transcription	NH-A	brain
4	chr2:133390000-133403200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:133390200-133394800	Weak transcription	Stomach Mucosa	stomach
6	chr2:133390200-133395800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr2:133390200-133403200	Weak transcription	Esophagus	oesophagus
8	chr2:133390200-133412600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr2:133390400-133395600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr2:133390400-133402000	Weak transcription	Fetal Kidney	kidney
11	chr2:133390400-133413800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr2:133390400-133423800	Weak transcription	A549	lung
13	chr2:133390600-133398800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr2:133390800-133395800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr2:133390800-133402800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr2:133390800-133405400	Weak transcription	Duodenum Mucosa	Duodenum
17	chr2:133391200-133399400	Weak transcription	Fetal Intestine Small	intestine
18	chr2:133393400-133394200	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr2:133393400-133394600	Enhancers	Liver	Liver
20	chr2:133393400-133394800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr2:133393400-133395600	Enhancers	Fetal Heart	heart
22	chr2:133393600-133394600	Enhancers	Rectal Mucosa Donor 29	rectum
23	chr2:133393600-133394600	Enhancers	Rectal Smooth Muscle	rectum
24	chr2:133393600-133394800	Enhancers	Fetal Stomach	stomach
25	chr2:133393600-133395000	Enhancers	Stomach Smooth Muscle	stomach
26	chr2:133393800-133394400	Enhancers	Colon Smooth Muscle	Colon
27	chr2:133393800-133394600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:133393800-133394600	Enhancers	Left Ventricle	heart
29	chr2:133393800-133394800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
30	chr2:133393800-133394800	Enhancers	Duodenum Smooth Muscle	Duodenum
31	chr2:133393800-133395400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr2:133393800-133395600	Enhancers	HSMMtube	muscle
33	chr2:133393800-133396200	Enhancers	Pancreas	Pancrea

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